Files in timothy-barry/sceptre
Analysis of Single-Cell CRISPR Screen Data

.Rbuildignore

.github/.gitignore

.github/workflows/check-standard.yaml

.gitignore

DESCRIPTION

NAMESPACE

NEWS.md R/RcppExports.R R/assign_grna_functions.R R/association_testing_functions_v2.R R/aux_functions.R R/cellwise_qc_functs.R R/check_functions.R R/data.R R/getters_and_setters.R R/import_functs.R R/medium_level_functs_v2.R R/mixture_model_functs.R R/neg_control_functions.R R/ondisc_functs.R R/pair_constructor_functs.R R/pairwise_qc_functs.R R/plotting_functions.R R/precomputation_functions.R R/preprocessing_functions.R R/qq_plot_helpers.R R/s4_analysis_functs_1.R R/s4_analysis_functs_2.R R/s4_class.R R/s4_helpers.R R/sceptre.R R/test_functs.R README.Rmd README.md

_pkgdown.yml

data-raw/DATASET_gene_table.R data-raw/DATASET_highmoi_example_data.R data-raw/DATASET_lowmoi_example_data.R

data/gene_position_data_frame_grch37.rda

data/gene_position_data_frame_grch38.rda

data/grna_target_data_frame_highmoi.rda

data/highmoi_example_data.rda

data/lowmoi_example_data.rda

docs/404.html

docs/LICENSE-text.html

docs/LICENSE.html

docs/articles/calibration_check.png

docs/articles/discovery_analysis.png

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docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

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docs/reference/assign_grnas.html

docs/reference/construct_cis_pairs.html

docs/reference/construct_positive_control_pairs.html

docs/reference/construct_trans_pairs.html

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docs/reference/gene_position_data_frame_grch38.html

docs/reference/get_grna_assignments.html

docs/reference/get_response_matrix.html

docs/reference/get_result.html

docs/reference/grna_target_data_frame_highmoi.html

docs/reference/highmoi_example_data.html

docs/reference/import_data.html

docs/reference/import_data_from_cellranger.html

docs/reference/import_data_from_parse.html

docs/reference/index.html

docs/reference/lowmoi_example_data.html

docs/reference/plot-sceptre_object-method.html

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docs/reference/read_ondisc_backed_sceptre_object.html

docs/reference/run_calibration_check.html

docs/reference/run_discovery_analysis.html

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docs/search.json

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inst/CITATION

inst/extdata/highmoi_example/gem_group_1/barcodes.tsv.gz

inst/extdata/highmoi_example/gem_group_1/features.tsv.gz

inst/extdata/highmoi_example/gem_group_1/matrix.mtx.gz

inst/extdata/highmoi_example/gem_group_2/barcodes.tsv.gz

inst/extdata/highmoi_example/gem_group_2/features.tsv.gz

inst/extdata/highmoi_example/gem_group_2/matrix.mtx.gz

inst/extdata/parse_example/all_genes.csv

inst/extdata/parse_example/all_grnas.csv

inst/extdata/parse_example/gene_mat.mtx

inst/extdata/parse_example/grna_mat.mtx

man/assign_grnas.Rd man/construct_cis_pairs.Rd man/construct_positive_control_pairs.Rd man/construct_trans_pairs.Rd

man/figures/hex.jpg

man/gene_position_data_frame_grch38.Rd man/get_grna_assignments.Rd man/get_response_matrix.Rd man/get_result.Rd man/grna_target_data_frame_highmoi.Rd man/highmoi_example_data.Rd man/import_data.Rd man/import_data_from_cellranger.Rd man/import_data_from_parse.Rd man/lowmoi_example_data.Rd man/plot-sceptre_object-method.Rd man/plot_assign_grnas.Rd man/plot_covariates.Rd man/plot_grna_count_distributions.Rd man/plot_response_grna_target_pair.Rd man/plot_run_calibration_check.Rd man/plot_run_discovery_analysis.Rd man/plot_run_power_check.Rd man/plot_run_qc.Rd man/print-sceptre_object-method.Rd man/read_ondisc_backed_sceptre_object.Rd man/run_calibration_check.Rd man/run_discovery_analysis.Rd man/run_power_check.Rd man/run_qc.Rd man/sceptre-package.Rd man/set_analysis_parameters.Rd man/write_outputs_to_directory.Rd

sceptre.Rproj

src/RcppExports.cpp

src/check_functions.cpp

src/compute_nb_size_param_functions.cpp

src/generate_samples_functions.cpp

src/low_level_distilled_test.cpp

src/low_level_full_test.cpp

src/mixture_functs.cpp

src/negative_control_functions.cpp

src/pair_construction_functs.cpp

src/pairwise_qc.cpp

src/shared_low_level_functions.cpp

src/shared_low_level_functions.h

src/sparse_matrix_functs.cpp

tests/testthat.R tests/testthat/helper-mock-data.R tests/testthat/test-assign_grnas.R tests/testthat/test-aux_functions.R tests/testthat/test-check_functions.R tests/testthat/test-mock-data-functions.R tests/testthat/test-plotting_functions.R tests/testthat/test-preprocessing_functs.R tests/testthat/test-run_qc.R tests/testthat/test-s4_analysis_functs_1.R tests/testthat/test-s4_analysis_functs_2.R tests/testthat/test-s4_helpers.R

vignettes/.gitignore

vignettes/calibration_check.png

vignettes/discovery_analysis.png

vignettes/grna_count_assignments.png

vignettes/grna_count_distribution.png

vignettes/pipeline_schematic.png

vignettes/power_check.png

vignettes/qc.png

vignettes/sceptre.Rmd

vignettes/update_vignette.sh

timothy-barry/sceptre documentation built on Jan. 20, 2025, 3:43 a.m.

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timothy-barry/sceptre
Analysis of Single-Cell CRISPR Screen Data

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Analysis of Single-Cell CRISPR Screen Data

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timothy-barry/sceptre Analysis of Single-Cell CRISPR Screen Data

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timothy-barry/sceptre
Analysis of Single-Cell CRISPR Screen Data

Files in timothy-barry/sceptre
Analysis of Single-Cell CRISPR Screen Data